Dynalign pipeline

Dynalign specifications

Information


Unique identifier OMICS_20023
Name Dynalign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Two sequences.
Output data A sequence alignment and a common structure for the two input sequences.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Douglas Turner <>

Additional information


Dynalign is fully incorporated into the RNAstructure package.

Publication for Dynalign

Dynalign IN pipelines

 (5)
2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] the exact alignment is constrained. highly probable nucleotide alignments, exceeding a specified threshold, are forced to occur in the simultaneous prediction of the alignment and common sequence., dynalign [5,6] is an implementation of the sankoff algorithm that predicts the lowest free energy structure common to two sequences. to make the calculation time tractable, a restriction […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] sequences. since these require significantly more time than the shorter trna sequences the overall impact of the speed-up is very significant and in fact increases the length of sequences on which dynalign can be deployed., the memory requirements for the two methods are compared in table 5, where the minimum, maximum, and average memory (in megabytes) required for the 100 sequence pairs […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] requirements are as reported in the size entry of linux ps command after all requisite dynamic allocations are done. this number corresponds to approximate value of virtual memory usage of the (dynalign) process. the tabulated numbers indicate that the proposed method also offers a memory advantage. as might be anticipated, the advantage is relatively minor for short sequence lengths (e.g. […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] significant for longer sequences (e.g. 5s rnas). the savings for longer sequences are particularly attractive since often memory is a limitation that restricts the length of sequences for which dynalign may be utilized., for benchmarking purposes, the implementation of the new principled alignment constraint (using the threshold of posterior co-incidence probabilities) and the previous […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] dynalign may be utilized., for benchmarking purposes, the implementation of the new principled alignment constraint (using the threshold of posterior co-incidence probabilities) and the previous dynalign banding constraint (m constraint) [35] were also compared against three other dynamic programming algorithms. the three other programs are foldalign [33], which uses a free energy-based […]

Dynalign institution(s)
Department of Chemistry, University of Rochester, Rochester, NY, USA
Dynalign funding source(s)
Supported by NIH grant GM22939. D.H.M. is a trainee in the medical scientist training program, NIH grant 5T32 GM07356.

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